annotateRepeats: Annotate repetitive elements

In Aufiero/circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

Annotate repetitive elements

Description

The function annotateRepeats() annotates repetitive elements located in the region flanking the back-spliced junctions of each circRNA. Repetitive elements are provided by AnnotationHub storage which collected repeats from RepeatMasker database. See AnnotationHub and http://www.repeatmasker.org for more details. An empty list is returned if none overlapping repeats are found.

Usage

annotateRepeats(targets, annotationHubID = "AH5122", complementary = TRUE)

Arguments

targets	A list containing the target regions to analyze. It can be generated with getSeqsFromGRs.
annotationHubID	A string specifying the AnnotationHub id to use. Type data(ahRepeatMasker) to see all possible options. E.g. if AH5122 is specified, repetitive elements from Homo sapiens, genome hg19 will be downloaded and annotated. Default value is "AH5122".
complementary	A logical specifying whether to filter and report only back-spliced junctions of circRNAs which flanking introns contain complementary repeats, that is, repeats belonging to a same family but located on opposite strands.

Value

A list.

Examples

# Load data frame containing detected back-spliced junctions
data("mergedBSJunctions")

# Load short version of the gencode v19 annotation file
data("gtf")

# Annotate the first back-spliced junctions
annotatedBSJs <- annotateBSJs(mergedBSJunctions[1, ], gtf)

# Get genome
if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)){

genome <- BSgenome::getBSgenome("BSgenome.Hsapiens.UCSC.hg19")

# Retrieve targets
targets <- getSeqsFromGRs(
    annotatedBSJs,
    genome,
    lIntron = 200,
    lExon = 10,
    type = "ie"
    )

# Annotate repeats

# repeats <- annotateRepeats(targets, annotationHubID  = "AH5122", complementary = TRUE)

}

Aufiero/circRNAprofiler documentation built on Oct. 31, 2023, 1:18 a.m.